In 2286, when Earth was threatened by the Whale probe, Section 31 took a cloaked ship near it and acquired several components from the probe. They then anonymously sent information on what they knew of the components to Starfleet Intelligence, in hopes that Starfleet Intelligence could adapt it to engine technology. When Starfleet Intelligence was successful, Section 31 intercepted them and stole all their work. ("Forbidden Crossing, Part I")

In 2384, additional technical components became available to the Phoenix-X's transwarp drive. These additional components, from the Whale probe itself, allowed a faster kind of transwarp for the Phoenix-X. Thus, Section 31 put plans into motion where the Phoenix-X would visit the Andromeda Galaxy and make first contact with native species there. AdmiralTheseus, a Section 31 operative, took part in the mission due to the true nature of Section 31's intentions - which were to gain the Kelvans as personal allies. Unfortunately, this was not successful, and instead of returning home with allies, Theseus acquired Omega molecules, safely suspended within a chamber, inside of an Andromedan android body. ("Forbidden Crossing, Parts I, II, III")

In 2383, Agent Tolleson told Rodney Brickenhouser that PresidentKorvin Mot should be replaced by vice president Kaenar Korban to ensure a Federation victory in the Coalition War. After Brickenhouser questioned whether or not Section 31 had that reach, Tolleson asserted that the agency had manipulated Jonathan Archer into ensuring the agency's placement within the Federation Charter. Tolleson then went on to suggest that the 2380 election of Korvin Mot had also been ensured by the agency, and the long range sensor readings from Minark that prompted Starfleet into sending an expedition force were also part of the agency's recent activities. ("The Forgotten Planet")

In mid-2383, Agent Tolleson told Rodney Brickenhouser to leave Paris, telling him that their plan to remove Mot from power was rapidly approaching. He later contacted So'janAdmiralDa'note to give him the codes to Earth's automated defenses. Section 31 had been continually leaking information to the Coalition to help weaken Mot's Administration, allowing them to dispose of the president in favor (as they saw it) a "stronger" leader. ("Obsession")

In a slightly parallel universe, Section 31 has formed a secret ad hoc alliance with the CardassianObsidian Order and the RomulanTal Shiar for the purpose of evaluating any threats from the Gamma Quadrant. Prior to the joint Romulan-Cardassian fleet that was sent to the Omarion Nebula, an initial Galor-class ship named the Vetara was modified as an unmanned exploratory ship and was tasked to explore the Gamma Quadrant. Prior to reaching the Bajoran wormhole, this ship disappeared and was presumed lost. It is later discovered that the ship was whisked away to the Delta Quadrant in a similar manner to the USS Voyager.

Starfleet Intelligence launched a classified mission to a dark matter nebula, investigating a distress call from the SS Anbar, but also to determine whether an incursion by Bluegill parasites had taken place. TNG: "Conspiracy". Though survivors were located and rescued, the mission was compromised when a bluegill operative, Phillipe Ermez, blew open a boarding pod that had penetrated the Anbar. Both the Anbar, along with the ship that had come to rescue them, The Excelsior, were inundated by the parasites. The Excelsior successfully escaped, and got rid of the bluegill intruders, but it fell to Section 31 to determine the bluegill objectives, and uncover why they hadn't begun their invasion of the Federation. The reason became known as "The Sword of Damocles". The Bluegills had encountered the Borg, and begun an all or nothing battle for the control of the Milky Way. So far, the war had been fought to a standstill, with neither side gaining an advantage. But, the day that one side triumphed over the other, the sword would fall, and the survivors would be killed or enslaved.

The task of monitoring the sword fell to Section 31 senior operative General Isaac Brahms. An extremely dedicated individual, Brahms was obsessed with preserving the sword as long as possible, no matter the cost. In his quest to prevent the sword from falling, he has gone so far as destroying a Galaxy-class starship, the USS Yorktown, and ordering the slaughter of the New Victoria colony, nearly 10,000 civilians. Brahms has also utilized genetic controls, as well as assasination squads.

The true name of Section 31 is unknown. The Obsidian Order is under the impression that the humans simply call it "The Bureau." It may be shorthand for Bureau of Interstellar Security, or Bureau of Interstellar Stability. The Bureau was created pursuant to Article 14, Section 31 of the Starfleet Charter. (Into The Field)

In Star Trek: Phoenix-X, Section 31 was never originally part of the beginning concept. The organization wasn't incorporated into the story and backstory until the second season. They were first mentioned by Theseus in "Jumpers, Part I". Mission-givers Elena and Nelkast started out as Theseus' assistants in the season three episode "Possible Regret" and didn't start giving missions as admitted Section 31 agents until the episode "Departments".